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- PDB-6khz: p62/SQSTM1 ZZ domain with Gly-peptide -

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Basic information

Entry
Database: PDB / ID: 6khz
Titlep62/SQSTM1 ZZ domain with Gly-peptide
ComponentsSequestosome-1
KeywordsSIGNALING PROTEIN / p62
Function / homology
Function and homology information


brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / Lewy body / response to mitochondrial depolarisation / aggrephagy / amphisome / negative regulation of toll-like receptor 4 signaling pathway / pexophagy ...brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / Lewy body / response to mitochondrial depolarisation / aggrephagy / amphisome / negative regulation of toll-like receptor 4 signaling pathway / pexophagy / regulation of protein complex stability / autophagy of mitochondrion / endosome organization / non-membrane-bounded organelle assembly / molecular sequestering activity / phagophore assembly site / regulation of mitochondrion organization / aggresome / regulation of canonical NF-kappaB signal transduction / ubiquitin-modified protein reader activity / Nuclear events mediated by NFE2L2 / autolysosome / K63-linked polyubiquitin modification-dependent protein binding / intracellular non-membrane-bounded organelle / endosomal transport / temperature homeostasis / immune system process / mitophagy / autophagosome / positive regulation of autophagy / energy homeostasis / signaling adaptor activity / inclusion body / sperm midpiece / negative regulation of protein ubiquitination / protein sequestering activity / p75NTR recruits signalling complexes / PINK1-PRKN Mediated Mitophagy / Pexophagy / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / sarcomere / SH2 domain binding / molecular condensate scaffold activity / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / macroautophagy / protein kinase C binding / positive regulation of protein localization to plasma membrane / ionotropic glutamate receptor binding / P-body / protein catabolic process / protein localization / receptor tyrosine kinase binding / PML body / autophagy / Interleukin-1 signaling / protein import into nucleus / KEAP1-NFE2L2 pathway / Signaling by ALK fusions and activated point mutants / late endosome / protein-macromolecule adaptor activity / Neddylation / signaling receptor activity / ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / cell differentiation / intracellular signal transduction / positive regulation of protein phosphorylation / positive regulation of apoptotic process / intracellular membrane-bounded organelle / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / UBA domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Ubiquitin associated domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. ...Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / UBA domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Ubiquitin associated domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / UBA-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKwon, D.H. / Kim, L. / Song, H.K.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Use of the LC3B-fusion technique for biochemical and structural studies of proteins involved in the N-degron pathway.
Authors: Kim, L. / Kwon, D.H. / Heo, J. / Park, M.R. / Song, H.K.
History
DepositionJul 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sequestosome-1
B: Sequestosome-1
C: Sequestosome-1
D: Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,17612
Polymers21,6534
Non-polymers5238
Water00
1
A: Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5443
Polymers5,4131
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3570 Å2
MethodPISA
2
B: Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5443
Polymers5,4131
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30 Å2
ΔGint-7 kcal/mol
Surface area3670 Å2
MethodPISA
3
C: Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5443
Polymers5,4131
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30 Å2
ΔGint-6 kcal/mol
Surface area3200 Å2
MethodPISA
4
D: Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5443
Polymers5,4131
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.979, 113.979, 113.979
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein/peptide
Sequestosome-1 / p62/SQSTM1 / EBI3-associated protein of 60 kDa / p60 / Phosphotyrosine-independent ligand for the ...p62/SQSTM1 / EBI3-associated protein of 60 kDa / p60 / Phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa / Ubiquitin-binding protein p62


Mass: 5413.129 Da / Num. of mol.: 4 / Fragment: ZZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SQSTM1, ORCA, OSIL / Production host: Escherichia coli (E. coli) / References: UniProt: Q13501
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Sequence detailsThe residues 121-125 GEEED is chimeric sequence.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.17 M Ammonium sulfate, 0.085 M Sodium cacodylate trihydrate pH 6.5, 22-30 % w/v Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 6200 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.054 / Net I/σ(I): 19.8
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.86 / Num. unique obs: 6200

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YP7

5yp7


Resolution: 2.8→40.3 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2873 --
Rwork0.2348 --
obs0.24 6200 100 %
Refinement stepCycle: LAST / Resolution: 2.8→40.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1401 0 8 0 1409

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